A Practical Primer in Human Complex Genetics was originally written for the the Genetic Epidemiology course organized by the Master Epidemiology of Utrecht University, but can be used as a practical guide and companion to learning and doing a genome-wide association study (GWAS).
It is available as GitBook and HTML. A PDF and EPUB version is forthcoming.
This book was made possible by the kind help of Caspar J. van Lissa who wrote an excellent instruction through an example GitBook https://cjvanlissa.github.io/gitbook-demo/.
_Version:_ v2.2.6</br>
_Last update:_ 2024-04-15</br>
_Written by:_ Sander W. van der Laan (s.w.vanderlaan-2[at]umcutrecht.nl).
**MoSCoW To-Do List**
The things we Must, Should, Could, and Would have given the time we have.
_M_
- [x] `M` create a separate CoCalc version
~- [] `M` add in full installation instructions for UBUNTU > DROPPED~
- [x] `M` add in full installation instructions for macOS
- [x] `M` create chapter on CoCalc
- [x] `M` redesign 'Getting Started' chapter
- [x] `M` add proper team-page
- [x] `M` fix regional association plotting
- [x] `M` fix issue with api of Two Sample MR > run the codes.
- [x] `M` fix issue with `api of Two Sample MR`cat: /Users/USERNAME/Desktop/practical/gwas/data.assoc.logistic.clumped: No such file or directory` - this was not run yet
- [x] `M` fix images per header in GitBook (not showing)
- [] `M` conditional analysis
- [] `M` statistical finemapping
- [] `M` colocalization with formal testing
- [x] `M` MRbase tutorial > dropped in favor of Two Sample MR > added a quick-and-dirty fix for now
- [] `M` Add partial recreation of the Cystatin C MR study
- [x] `M` overall rendering too slow, paste in images as figure instead of on the fly generating
- [] `M` fix issue with PDF creation
- [] `M` fix issue with EPUB creation
- [] `M` fix issue with EPUB creation and images
- [] `M` get ISBN number
- [] `M` Upgrade to Quatro - seems to work better in many respects; also adds interactivity https://quarto.org/docs/books/. This will probably fix the PDF and EPUB creation issues, as well as the image display issues.
_S_
- [] `S` meta-analysis with dummy data
- `S` HPC version with MetaGWASToolKit
- `S` including stratified QQ plots
- `S` stand-alone version with METAL
- [] `S` add online imputation chapter
- [] `S` fix images per header in EPUB
- [] `S` PDF is not formatted properly (text runs over)
- [] `S` EPUB is not formatted properly (text runs over)
- [] `S` different setup for the chapter Additional chapters (this as a Apendix)
- [x] `S` fix the way the team is displayed
- [] `S` fix book cover > version 2024 'quick and dirty'
- https://www.designhill.com/design-blog/the-perfect-ebook-cover-size-guide-and-publishing-tips/
- https://snappa.com/blog/ebook-cover-size/
- https://kdp.amazon.com/en_US/help/topic/G200645690.
- [] `S` add in chapter on liftOver
_C_
- [] `C` GWASToolKit
- [] `C` PlaqView lookups
- [] `C` Different font type in PDF
_W_
~- [] `W` add in full installation instructions for Windows > DROPPED~
- [x] `W` add favicon and Apple-touch-icon
- https://iconifier.net
**Changes log**
* v2.2.5 Name change in preparation of the Standalone version.
* v2.2.4 Version fix on the main page. Fixed error on display of questions for TwoSample MR in Answer-chapter. Fixed command in WTCCC1 association chapter.
* v2.2.4 Removed code block in FUMA-chapter. Added quick-and-dirty fix for MRBase. Added Answers to questions.
* v2.2.3 Fixes to the rendering of the book. Fixes to the references. Fixed issue with FUMA input file. Splitted the WTCCC1 analyses in 3 parts, first introduction, then quality control, finally association testing.
* v2.2.2 Small fix to remove `knitr` codes. Fixed errors in `opts$chunks` for `knitr` and `rmarkdown` regarding 'echo'.
* v2.2.1 Small fixes to references. Added book cover. Added favicon and Apple-touch-icon.
* v2.2.0 Created a full CoCalc version, and a separate Standalone version.
* v2.1.2 Small fix to directory reference.
* v2.1.1 Finalized CoCalc instructions. Added Team chapter. Fixed issue with Two-Sample MR. Fixed issue with regional association plotting. Checked Questions and Answers. Edited the To-Do list
* v2.1.0 Added CoCalc instructions. Added Standalone instructions. Added chapter on used-programs. Re-organized 'Getting Started' chapter. Updated To-Do list in readme.
* v2.0.6 Fixes to the visualization chapter where data was not properly loaded. Fix to the references in the WTCCC1 chapter where they were not properly generated.
* v2.0.5 Added all header-images. Fixed references to tables and figures.
* v2.0.4 Added WTCCC1 introduction; added WTCCC1 analyses and visualization. Add post-GWAs chapter.
* v2.0.3 Added GWAS visualization.
* v2.0.2 Added GWAS testing. Updates to saving of plots. Re-organization of data.
* v2.0.1 Fixed standalone instructions. Fixed dummy GWAS project.
* v1.0.0 Initial version.
Copyright 1979-2024. All rights reserved. Sander W. van der Laan | s.w.vanderlaan [at] gmail.com | https://vanderlaanand.science{target="_blank"}. Published with bookdown{target="_blank"}.